Molecular sensor

A molecular sensor or chemosensor is a molecule that interacts with an analyte to produce a detectable change. Molecular sensors combine molecular recognition with some form of reporter so the presence of the guest can be observed. The term supramolecular analytical chemistry has recently been coined to describe the application of molecular sensors to analytical chemistry.
Early examples of molecular sensors are crown ethers with large affinity for sodium ions but not for potassium and forms of metal detection by so-called complexones which are traditional pH indicators retrofitted with molecular groups sensitive to metals. This receptor-spacer-reporter concept is a recurring theme often with the reporter displaying photoinduced electron transfer.One example is a sensor sensitive to heparin.

Magnetism

In physics, magnetism is one of the phenomena by which materials exert attractive or repulsive forces on other materials. Some well-known materials that exhibit easily detectable magnetic properties (called magnets) are nickel, iron, cobalt, and their alloys; however, all materials are influenced to greater or lesser degree by the presence of a magnetic field.
Magnetism also has other manifestations in physics, particularly as one of the two components of electromagnetic waves such as light

Photoisomerization

In chemistry, photoisomerization is molecular behavior in which structural change between isomers is caused by photoexcitation. Both reversible and irreversible photoisomerization reactions exist. However, the word "photoisomerization" usually indicates a reversible process. Photoisomerizable molecules are already put to practical use, for instance, in pigments for rewritable CDs, DVDs, and 3D optical data storage solutions. In addition, recent interest in photoisomerizable molecules has been aimed at molecular devices, such as molecular switches, molecular motors, and molecular electronics.
Photoisomerization behavior can be roughly categorized into two classes: trans (or E) and cis (or Z) conversion, and open ring and closed ring transition. Instances of the former include stilbene and azobenzene. This class of compounds has a double bond, and rotation or inversion around the double bond affords isomerization between the two states. Examples of the latter include fulgide and diarylethene. These types of compounds undergo bond cleavage and bond creation upon irradiation with particular wavelengths of light

Data storage and processing

Supramolecular chemistry has been used to demonstrate computation functions on a molecular scale. In many cases, photonic or chemical signals have been used in these components, but electrical interfacing of these units has also been shown by supramolecular signal transduction devices. Data storage has been accomplished by the use of molecular switches with photochromic and photoisomerizable units, by electrochromic and redox-switchable units, and even by molecular motion. Synthetic molecular logic gates have been demonstrated on a conceptual level. Even full-scale computations have been achieved by semi-synthetic DNA computers.

Medicine

Supramolecular chemistry is also important to the development of new pharmaceutical therapies by understanding the interactions at a drug binding site. The area of drug delivery has also made critical advances as a result of supramolecular chemistry providing encapsulation and targeted release mechanisms. In addition, supramolecular systems have been designed to disrupt protein-protein interactions that are important to cellular function

Catalysis

Catalysis is the process by which the rate of a chemical reaction (or biological process) is increased by means of the addition of a species known as a catalyst to the reaction. What makes a catalyst different from a chemical reagent is that whilst it participates in the reaction, it is not consumed in the reaction. That is, the catalyst may undergo several chemical transformations during the reaction, but at the conclusion of the reaction, the catalyst is regenerated unchanged. As a catalyst is regenerated in a reaction, often only a very small amount is needed to increase the rate of the reaction.

Materials technology

Supramolecular chemistry and molecular self-assembly processes in particular have been applied to the development of new materials. Large structures can be readily accessed using bottom-up synthesis as they are composed of small molecules requiring fewer steps to synthesize. Thus most of the bottom-up approaches to nanotechnology are based on supramolecular chemistry.

Biologically-derived units

The extremely strong complexation between avidin and biotin is instrumental in blood clotting, and has been used as the recognition motif to construct synthetic systems.
The binding of enzymes with their cofactors has been used as a route to produce modified enzymes, electrically contacted enzymes, and even photoswitchable enzymes.
DNA has been used both as a structural and as a functional unit in synthetic supramolecular systems.

Photo-/electro-chemically active units

Porphyrins, and phthalocyanines have highly tunable photochemical and electrochemical activity as well as the potential for forming complexes.
Photochromic and photoisomerizable groups have the ability to change their shapes and properties (including binding properties) upon exposure to light.
TTF and quinones have more than one stable oxidation state, and therefore can be switched with redox chemistry or electrochemistry. Other units such as benzidine derivatives, viologens groups and fullerenes, have also been utilized in supramolecular electrochemical devices.

Structural units of Supramolecular Chemistry

Many supramolecular systems require their components to have suitable spacing and conformations relative to each other, and therefore easily-employed structural units are required.
Commonly used spacers and connecting groups include polyether chains, biphenyls and triphenyls, and simple alkyl chains. The chemistry for creating and connecting these units is very well understood.
nanoparticles, nanorods, fullerenes and dendrimers offer nanometer-sized structure and encapsulation units.
Surfaces can be used as scaffolds for the construction of complex systems and also for interfacing electrochemical systems with electrodes. Regular surfaces can be used for the construction of self-assembled monolayers and multilayers

Calixarene

A calixarene is a macrocycle or cyclic oligomer based on a hydroxyalkylation product of a phenol and an aldehyde . The word calixarene is derived from calix or chalice because this type of molecule resembles a vase and from the word arene that refers to the aromatic building block. Calixarenes have hydrophobic cavities that can hold smaller molecules or ions and belong to the class of cavitands known in Host-guest chemistry. Calixarene nomenclature is straightforward and involves counting the number of repeating units in the ring and include it in the name. A calix arene has 4 units in the ring and a calix arene has 6. A substituent in the meso position Rb is added to the name with a prefix C- as in C-methylcalix arene.

Cyclodextrins

Cyclodextrins (sometimes called cycloamyloses) make up a family of cyclic oligosaccharides, composed of 5 or more α-D-glucopyranoside units linked 1->4, as in amylose (a fragment of starch). The 5-membered macrocycle is not natural. Recently, the largest well-characterized cyclodextrin contains 32 1,4-anhydroglucopyranoside units, while as a poorly characterized mixture, even at least 150-membered cyclic oligosaccharides are also known. Typical cyclodextrins contain a number of glucose monomers ranging from six to eight units in a ring, creating a cone shape. thus denoting:
α-cyclodextrin: six membered sugar ring molecule
β-cyclodextrin: seven sugar ring molecule
γ-cyclodextrin: eight sugar ring molecule
Cyclodextrins are produced from starch by means of enzymatic conversion. Over the last few years they have found a wide range of applications in food, pharmaceutical and chemical industries as well as agriculture and environmental engineering. It is also the chief active compound found in Procter and Gamble's deodorizing product "Febreze".

Macrocycles

Macrocycles are very useful in supramolecular chemistry, as they provide whole cavities that can completely surround guest molecules and may be chemically modified to fine-tune their properties.
Cyclodextrins, calixarenes, cucurbiturils and crown ethers are readily synthesized in large quantities, and are therefore convenient for use in supramolecular systems.
More complex cyclophanes, and cryptands can be synthesized to provide more taliored recognition properties.

Synthetic recognition motifs of Supramolecular Chemistry

The pi-pi charge-transfer interactions of bipyridinium with dioxyarenes or diaminoarenes have been used extensively for the construction of mechanically interlocked systems and in crystal engineering.
The use of crown ether binding with metal or ammonium cations is ubiquitous in supramolecular chemistry.
The formation of carboxylic acid dimers and other simple hydrogen bonding interactions.
The complexation of bipyridines or tripyridines with ruthenium, silver or other metal ions is of great utility in the construction of complex architectures of many individual molecules.
The complexation of porphyrins or phthalocyanines around metal ions gives access to catalytic, photochemical and electrochemical properties as well as complexation. These units are used a great deal by nature.

Molecular nanotechnology

Molecular nanotechnology (MNT) is the concept of engineering functional mechanical systems at the molecular scale. An equivalent definition would be "machines at the molecular scale designed and built atom-by-atom". This is distinct from nanoscale materials. Based on Richard Feynman's vision of miniature factories using nanomachines to build complex products (including additional nanomachines), this advanced form of nanotechnology (or molecular manufacturing. would make use of positionally-controlled mechanosynthesis guided by molecular machine systems. MNT would involve combining physical principles demonstrated by chemistry, other nanotechnologies, and the molecular machinery of life with the systems engineering principles found in modern macroscale factories. Its most well-known exposition is in the books of K. Eric Drexler particularly Engines of Creation. Detailed theoretical investigation, sections 4.3 and 4.4 below, have investigated the feasibility of molecular nanotechnology, but the topic remains controversial.

Molecular machine

A molecular machine has been defined as a discrete number of molecular components that have been designed to perform mechanical-like movements (output) in response to specific stimuli (input). It is often applied more generally to molecules that simply mimic functions at the macroscopic level. The term is also common in nanotechnology and a number of highly complex molecular machines have been proposed towards the goal of constructing a molecular assembler. Molecular machines can be divided into two broad categories: synthetic and biological.
Molecular systems that are able to shift a chemical or mechanical process away from equilibrium represent a potentially important branch of chemistry and nanotechnology. By definition these types of systems are examples of molecular machinery, as the gradient generated from this process is able to perform useful work.

Molecular Imprinting

In chemistry, molecular imprinting is a technique to create template-shaped cavities in polymer matrices with memory of the template molecules. This technique is based on the system used by enzymes for substrate recognition, which is called the "lock and key" model. The active binding site of an enzyme has a unique geometric structure that is particularly suitable for a substrate. A substrate that has a corresponding shape to the site is recognized by selectively binding to the enzyme, while an incorrectly shaped molecule that does not fit the binding site is not recognized.
In a similar way, molecularly imprinted materials are prepared using a template molecule and functional monomers that assemble around the template and subsequently get crosslinked to each other. The functional monomers, which are self-assembled around the template molecule by interaction between functional groups on both the template and monomers, are polymerized to form an imprinted matrix (commonly known in the scientific community as a molecularly imprinted polymer i.e. MIP). Then the template molecule is removed from the matrix under certain conditions, leaving behind a cavity complementary in size and shape to the template. The obtained cavity can work as a selective binding site for a specific template molecule.

Protein design

Protein design is the design of new protein molecules from scratch, or the deliberate design of a new molecule by making calculated variations on a known structure. The number of possible amino acid sequences is enormous, but only a subset of these sequences will fold reliably and quickly to a single native state. Protein design involves identifying such sequences, in particular those with a physiologically active native state. Protein design is a rational design technique used in protein engineering.
Protein design requires an understanding of the process by which proteins fold. In a sense it is the reverse of structure prediction: a tertiary structure is specified, and a primary sequence is identified which will fold to it.
Protein design is also referred to as inverse folding. From a physical point of view, the native state conformation of a protein is the free energy minimum for the protein chain, at least at biological temperatures (i.e. at temperatures between zero and a hundred degrees Celsius). Hence, designing a new protein involves the identification of the sequences which have the chosen structure as free energy minimum. This can be done by use of computer models, which, while simplifying the problem, are able to generate sequences to fold on the desired structure.
The design of minimalist computer models of proteins (lattice proteins), and the secondary structural modification of real proteins, began in the mid-1990s. The de novo design of real proteins became possible shortly afterwards, and the 21st century has seen the creation of small proteins with real biological function including catalysis and antiviral behaviour. There is great hope that the design of these and larger proteins will have application in medicine and bioengineering.

An artificial neuron

An artificial neuron is a mathematical function conceived as a crude model, or abstraction of biological neurons. Artificial neurons are the constitutive units in an artificial neural network. Depending on the specific model used, it can receive different names, such as semi-linear unit, Nv neuron, binary neuron, linear threshold function or McCulloch-Pitts neuron. The artificial neuron receives one or more inputs (representing the one or more dendrites) and sums them to produce an output (synapse). Usually the sums of each node are weighted, and the sum is passed through a non-linear function known as an activation function or transfer function. The transfer functions usually have a sigmoid shape, but they may also take the form of other non-linear functions, piecewise linear functions, or step functions. They are also often monotonically increasing, continuous, differentiable and bounded

Radar

Radar is a system that uses electromagnetic waves to identify the range, altitude, direction, or speed of both moving and fixed objects such as aircraft, ships, motor vehicles, weather formations, and terrain. The term RADAR was coined in 1941 as an acronym for Radio Detection and Ranging. The term has since entered the English language as a standard word, radar, losing the capitalization. Radar was originally called RDF (Radio Direction Finder) in the United Kingdom.
A radar system has a transmitter that emits either radio waves or (more usually these days) microwaves that are reflected by the target and detected by a receiver, typically in the same location as the transmitter. Although the signal returned is usually very weak, the signal can be amplified. This enables radar to detect objects at ranges where other emissions, such as sound or visible light, would be too weak to detect. Radar is used in many contexts, including meteorological detection of precipitation, measuring ocean surface waves, air traffic control, police detection of speeding traffic, and by the military

Medical Ultrasound

Ultrasound is cyclic sound pressure with a frequency greater than the upper limit of human hearing. Although this limit varies from person to person, it is approximately 20 kilohertz (20,000 hertz) in healthy, young adults and thus, 20 kHz serves as a useful lower limit in describing ultrasound. The production of ultrasound is used in many different fields, typically to penetrate a medium and measure the reflection signature or supply focused energy. The reflection signature can reveal details about the inner structure of the medium. The most well known application of this technique is its use in sonography to produce pictures of fetuses in the human womb. There are a vast number of other applications as well.

Bionics

Bionics (also known as biomimetics, biognosis, biomimicry, or bionical creativity engineering) is the application of biological methods and systems found in nature to the study and design of engineering systems and modern technology. The word "bionic" was coined by Jack E. Steele in 1958, possibly originating from the Greek word "βίον", pronounced "bion", meaning "unit of life" and the suffix -ic, meaning "like" or "in the manner of", hence "like life". Some dictionaries, however, explain the word as being formed from "biology" + "electronics".
The transfer of technology between lifeforms and synthetic constructs is, according to proponents of bionic technology, desirable because evolutionary pressure typically forces living organisms, including fauna and flora, to become highly optimized and efficient. A classical example is the development of dirt- and water-repellent paint (coating) from the observation that the surface of the lotus flower plant is practically unsticky for anything (the lotus effect).
Examples of bionics in engineering include the hulls of boats imitating the thick skin of dolphins; sonar, radar, and medical ultrasound imaging imitating the echolocation of bats.
In the field of computer science, the study of bionics has produced artificial neurons, artificial neural networks, and swarm intelligence. Evolutionary computation was also motivated by bionics ideas but it took the idea further by simulating evolution in silico and producing well-optimized solutions that had never appeared in nature.

Dynamic covalent chemistry

In dynamic covalent chemistry covalent bonds are broken and formed in a reversible reaction under thermodynamic control. While covalent bonds are key to the process the system is directed by noncovalent forces to form the lowest energy structures.

Molecular Borromean rings

Molecular Borromean rings are an example of a mechanically-interlocked molecular architecture in which three macrocycles are interlocked in such a way that breaking any macrocycle allows the others to disassociate. They are the smallest examples of Borromean rings. The synthesis of molecular Borromean rings was reported in 2004 by the group of J. Fraser Stoddart is made up of macrocycles formed from 2,6-diformylpyridine and diamine compounds complexed with zinc

Molecular knot

In chemistry, a molecular knot (knotane) is a mechanically-interlocked molecular architecture that is analogous to a macroscopic knot. A molecular knot in a trefoil knot configuration is chiral, having at least two enantiomers. Examples of naturally formed knotanes are DNA and certain proteins. Lactoferrin has an unusual biochemical reactivity compared to its linear analogue. Other synthetic molecular knots have a distinct globular shape and nanometer sized dimensions that make it potential building blocks in nanotechnology. Molecular knots are also referred to by some chemists as "knotanes". The term Knotane was coined by Fritz Vögtle et al in Angewandte Chemie International Edition in 2000 by analogy with rotaxane and catenane.The term however has yet to be adopted by IUPAC.

Rotaxane

A rotaxane is a mechanically-interlocked molecular architecture consisting of a "dumbbell shaped molecule" which is threaded through a "macrocycle" (see graphical representation). The name is derived from the Latin for wheel (rota) and axle (axis). The two components of a rotaxane are kinetically trapped since the ends of the dumbbell (often called stoppers) are larger than the internal diameter of the ring and prevent disassociation (unthreading) of the components since this would require significant distortion of the covalent bonds.
Much of the research concerning rotaxanes and other mechanically-interlocked molecular architectures, such as catenanes, has been focused on their efficient synthesis. However, examples of rotaxane have been found in biological systems including: cystine knots, cyclotides or lasso-peptides such as microcin J25 are protein, and a variety of peptides with rotaxane substructure.

Catenane

A catenane is a mechanically-interlocked molecular architecture consisting of two or more interlocked macrocycles. The interlocked rings cannot be separated without breaking the covalent bonds of the macrocycles. Catenane is derived from the Latin catena meaning "chain". They are conceptually related to other mechanically-interlocked molecular architectures, such as rotaxanes, molecular knots or molecular Borromean rings. Recently the terminology "mechanical bond" has been coined that describes the connection between the macrocycles of a catenane

Mechanically-interlocked molecular architectures

Mechanically-interlocked molecular architectures consist of molecules that are linked only as a consequence of their topology. Some noncovalent interactions may exist between the different components (often those that were utilized in the construction of the system), but covalent bonds do not. Supramolecular chemistry, and template-directed synthesis in particular, is key to the efficient synthesis of the compounds. Examples of mechanically-interlocked molecular architectures include catenanes, rotaxanes, molecular knots, and molecular Borromean rings.

Template-directed synthesis

Molecular recognition and self-assembly may be used with reactive species in order to pre-organize a system for a chemical reaction (to form one or more covalent bonds). It may be considered a special case of supramolecular catalysis. Noncovalent bonds between the reactants and a "template" hold the reactive sites of the reactants close together, facilitating the desired chemistry. This technique is particularly useful for situations where the desired reaction conformation is thermodynamically or kinetically unlikely, such as in the preparation of large macrocycles. This pre-organization also serves purposes such as minimizing side reactions, lowering the activation energy of the reaction, and producing desired stereochemistry. After the reaction has taken place, the template may remain in place, be forcibly removed, or may be "automatically" decomplexed on account of the different recognition properties of the reaction product. The template may be as simple as a single metal ion or may be extremely complex.

Molecular recognition and complexation

Molecular recognition is the specific binding of a guest molecule to a complementary host molecule to form a host-guest complex. Often, the definition of which species is the "host" and which is the "guest" is arbitrary. The molecules are able to identify each other using noncovalent interactions. Key applications of this field are the construction of molecular sensors and catalysis

Molecular self-assembly

Molecular self-assembly is the construction of systems without guidance or management from an outside source (other than to provide a suitable environment). The molecules are directed to assemble through noncovalent interactions. Self-assembly may be subdivided into intermolecular self-assembly (to form a supramolecular assembly), and intramolecular self-assembly (or folding as demonstrated by foldamers and polypeptides). Molecular self-assembly also allows the construction of larger structures such as micelles, membranes, vesicles, liquid crystals, and is important to crystal engineering.

Thermodynamics

Supramolecular chemistry deals with subtle interactions, and consequently control over the processes involved can require great precision. In particular, noncovalent bonds have low energies and often no activation energy for formation. As demonstrated by the Arrhenius equation, this means that, unlike in covalent bond-forming chemistry, the rate of bond formation is not increased at higher temperatures. In fact, chemical equilibrium equations show that the low bond energy results in a shift towards the breaking of supramolecular complexes at higher temperatures.
However, low temperatures can also be problematic to supramolecular processes. Supramolecular chemistry can require molecules to distort into thermodynamically disfavored conformations (e.g. during the "slipping" synthesis of rotaxanes), and may include some covalent chemistry that goes along with the supramolecular. In addition, the dynamic nature of supramolecular chemistry is utilized in many systems (e.g. molecular mechanics), and cooling the system would slow these processes

Definition of Supramolecular Chemistry

Supramolecular chemistry refers to the area of chemistry that focuses on the noncovalent bonding interactions of molecules. While traditional chemistry focuses on the covalent bond, supramolecular chemistry examines the weaker and reversible noncovalent interactions between molecules. These forces include hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, pi-pi interactions and electrostatic effects. Important concepts that have been demonstrated by supramolecular chemistry include molecular self-assembly, folding, molecular recognition, host-guest chemistry, mechanically-interlocked molecular architectures, and dynamic covalent chemistry. The study of non-covalent interactions is crucial to understanding many biological processes from cell structure to vision that rely on these forces for structure and function. Biological systems are often the inspiration for supramolecular research.